Research Article

An Exon-Based Comparative Variant Analysis Pipeline to Study the Scale and Role of Frameshift and Nonsense Mutation in the Human-Chimpanzee Divergence

Table 3

Insilico validation of exon-disrupting mutations.

FRPMSubject ScoreFunction description

CHIMP_X_139912: PREDICTED: Pan troglodytes similar to Cancer/testis antigen CT45-3

135199011-MONK_X_12447197.76
--CHIMP_X_139912159.41Pan troglodytes similar to Cancer/testis antigen CT45-3
135199011-HUMAN_X_807093140.8Cancer/testis antigen CT45-4 (CT45-4)
135199011-HUMAN_X_806975138.76Cancer/testis antigen CT45
135199011-HUMAN_X_807082138.76Cancer/testis antigen CT45-4 (CT45-4)
135199011-HUMAN_X_807113138.76Cancer/testis antigen CT45-6 (CT45-6)
135199011-HUMAN_X_806962137.58Cancer/testis antigen CT45-1 (CT45-1)
135199011-HUMAN_X_806970137.58Cancer/testis antigen CT45
135199011-MONK_X_12441136.48
135199011-CHIMP_X_140002132.22

CHIMP_X_144913: Melanoma-associated antigen C3

141390311141390248MONK_X_12774153.22
141390314141390248HUMAN_X_809204118.25Melanoma-associated antigen C3
--CHIMP_X_144913104.42Melanoma-associated antigen C3

CHIMP_X_144941: Melanoma-associated antigen C3

141392714 141393341-HUMAN_X_809214811.08Melanoma-associated antigen C3
141392714-HUMAN_X_809208504.96Melanoma-associated antigen C3
141392720-MONK_X_12788498.06Melanoma-associated antigen C2
141392720-HUMAN_X_809255489.78Melanoma-associated antigen C2
--CHIMP_X_144941415.82Melanoma-associated antigen C3

Chimp_x_91363: Homolog of Inhibitor of growth protein 1

70808615 7080855870808522 70808408MONK_17_129198197.85Inhibitor of growth protein 1
70808615 7080855870808522 70808408MONK_17_129202197.85Inhibitor of growth protein 1
70808615 7080855870808522 70808408MONK_17_129209197.85Inhibitor of growth protein 1
70808615 7080855870808522 70808408CHIMP_13_65452196.75Inhibitor of growth protein 1
70808615 7080855870808522 70808408HUMAN_13_720109196.75Inhibitor of growth protein 1
70808615 7080855870808522 70808408HUMAN_13_720111196.75Inhibitor of growth protein 1
70808615 7080855870808522 70808408HUMAN_13_720113196.75Inhibitor of growth protein 1
70808615 7080855870808522 70808408HUMAN_13_720115196.75Inhibitor of growth protein 1
7080854870808521 70808407RAT_16_143085188.7Inhibitor of growth family, member 1
7080854870808521 70808407DOG_22_9324186.9
7080854870808521 70808407MOUSE_8_2111806185.9Inhibitor of growth family, member 1
7080854870808521 70808407OPOSSUM_7_30919185.56Inhibitor of growth protein 1
7080854870808521 70808407COW_12_131559181.68Inhibitor of growth protein 1
--CHIMP_X_91363133.05
-70808403DANIO_9_335418127.32Hypothetical protein
-70808403DANIO_9_335470127.32Hypothetical protein
-70808403CHIMP_4_171949112.69Inhibitor of growth protein 2
-70808403COW_27_26326112.69
-70808403DOG_16_29019112.69
-70808403HUMAN_4_708541112.69Inhibitor of growth protein 2
-70808403MONK_5_172003112.69Inhibitor of growth family, member 1-like
-70808403OPOSSUM_5_33934112.69Inhibitor of growth protein 2
-70808403MOUSE_8_2166090111.86Inhibitor of growth family, member 2
-70808403RAT_16_84084110.51
-70808403DANIO_1_359897109.25Hypothetical protein
CHIMP_X_101234: Protocadherin-11 X-linked precursor

--CHIMP_X_101234516.68Protocadherin-11 X-linked precursor
91237579-HUMAN_Y_591033515.03Protocadherin-11 Y-linked precursor
--HUMAN_X_787233509.39Protocadherin-11 X-linked precursor
--CHIMP_X_101543479.57Protocadherin-11 X-linked precursor
--CHIMP_X_101362473.55Protocadherin-11 X-linked precursor

CHIMP_X_110683: Potassium channel tetramerisation domain containing 9-like

104937007104936803 104936929HUMAN_9_756669340.71
104937007104936803 104936929CHIMP_9_89777334.23
104937147104936946 104937072HUMAN_8_631149238.77
-104936946HUMAN_X_792440182.69Potassium channel tetramerisation domain containing 9-like
-104936946HUMAN_X_792443180.93Potassium channel tetramerisation domain containing 9-like
--CHIMP_X_11068393.45Potassium channel tetramerisation domain containing 9-like

CHIMP_X_110628: Testis-expressed sequence 13A protein

104742590-HUMAN_X_792407564.62Testis-expressed sequence 13A protein
--CHIMP_X_110628453.53Testis-expressed sequence 13A protein

CHIMP_1_136911 Tumor necrosis factor receptor superfamily member 18 precursor

1124826-HUMAN_1_800938181.65Tumor necrosis factor receptor superfamily member 18 precursor
--CHIMP_1_136911140Tumor necrosis factor receptor superfamily member 18 precursor
1124826-MONK_1_14977134.83Tumor necrosis factor receptor superfamily member 18 precursor
--MONK_1_1497723.57Tumor necrosis factor receptor superfamily member 18 precursor
--CHIMP_1_13691121.23Tumor necrosis factor receptor superfamily member 18 precursor

CHIMP_1_178077 Heat-shock protein beta-7 (hspb7)

-16234672HUMAN_1_816034160.14Heat-shock protein beta-7 (hspb7) (Cardiovascular heat shock protein)
-16234672HUMAN_1_816039160.14Heat-shock protein beta-7 (hspb7) (Cardiovascular heat shock protein)
--CHIMP_1_17807765.07Heat-shock protein beta-7 (hspb7) (Cardiovascular heat shock protein)

CHIMP_1_203439 Eyes absent homolog 3 (EC 3.1.3.48)

28236481-MONK_1_1984367.86Eyes absent homolog 3 (EC 3.1.3.48)
28236481-HUMAN_1_87063867.24Eyes absent homolog 3 (EC 3.1.3.48)
--CHIMP_1_20343958.79Eyes absent homolog 3 (EC 3.1.3.48)

CHIMP_1_226597 neuroblastoma breakpoint family, member 11 (NBPF11)

114514130-HUMAN_1_841875116.78Neuroblastoma breakpoint family, member 11 (NBPF11)
114514130-HUMAN_1_842031116.78Neuroblastoma breakpoint family, member 11 (NBPF11)
--CHIMP_1_22659796.53Neuroblastoma breakpoint family, member 11 (NBPF11)
--CHIMP_1_22635092.54Neuroblastoma breakpoint family, member 11 (NBPF11)
CHIMP_1_229134 Tropomyosin alpha-3 chain (Tropomyosin-3)

133314785-HUMAN_1_843860241.51Tropomyosin alpha-3 chain
133314785-MONK_1_57153224.17Tropomyosin alpha-3 chain
--CHIMP_1_22913494.16Tropomyosin alpha-3 chain

CHIMP_1_233220 Voltage-dependent R-type calcium channel subunit alpha-1E
(Voltage- gated calcium channel subunit alpha Cav2.3)
(Calcium channel, L type, alpha-1 polypeptide, isoform 6) (Brain calcium channel II)

161366683 -HUMAN_1_848676364.5Voltage-dependent R-type calcium channel subunit alpha-1E
161366683 -MONK_1_84331335.27Voltage-dependent R-type calcium channel subunit alpha-1E
161366683 -COW_16_164990306.65Calcium channel subunit alpha 1E
161366683 -RAT_13_76001300.14Voltage-dependent R-type calcium channel subunit alpha-1E
161366683 -MOUSE_1_2286080299.66Calcium channel, Voltage-dependent, R type, alpha 1E subunit
161366683 -DOG_7_48804298.94
--CHIMP_1_233220149.73PREDICTED: Pan troglodytes similar to Voltage-dependent calcium channel alpha-1E-3

CHIMP_1_235105 SOX-13 protein (Type 1 diabetes autoantigen ICA12) (Islet cell antigen 12)

184232055-HUMAN_1_850979134.55SOX-13 protein (Type 1 diabetes autoantigen ICA12) (Islet cell antigen 12)
--CHIMP_1_23510555.51SOX-13 protein (Type 1 diabetes autoantigen ICA12) (Islet cell antigen 12)

CHIMP_X_104156 ADP-ribosylation factoR-like protein 13A

100539703 -HUMAN_X_788396112.96ADP-ribosylation factoR-like protein 13A
100539703 -HUMAN_X_788399106.14ADP-ribosylation factoR-like protein 13A
- -CHIMP_X_10415697.94ADP-ribosylation factoR-like protein 13A
100539703 -MONK_X_1011593ADP-ribosylation factoR-like protein 13A

HUMAN_1_851772 Complement receptor type 1 precursor (c3b/C4b receptor) (CD35 antigen)

--HUMAN_1_85177290.18Complement receptor type 1 precursor (c3b/C4b receptor) (CD35 antigen)
--CHIMP_1_23587386.46Complement receptor type 1 precursor (c3b/C4b receptor) (CD35 antigen)
--CHIMP_1_23589586.46Pan troglodytes mrna sequence, end of ORF
205746964-CHIMP_1_23589185.81Complement receptor type 1 precursor (c3b/C4b receptor) (CD35 antigen)
--MONK_1_7529676.91Complement receptor type 1 precursor (c3b/C4b receptor) (CD35 antigen)
--HUMAN_1_85182175.98Complement C4b binding protein CR-1 like (Fragment)
205746964-CHIMP_1_23590574.1Pan troglodytes mrna sequence, end of ORF
205746964-CHIMP_1_23590974.1Pan troglodytes mrna sequence, end of ORF

HUMAN_1_851437 solute carrier family 26, member 9 isoform A

204150951-CHIMP_1_235519351.23Solute carrier family 26, member 9 isoform A
204150951-MONK_1_76747337.22Solute carrier family 26, member 9 isoform A
--HUMAN_1_851439252.06Solute carrier family 26, member 9 isoform A
HUMAN_1_837766 calcium activated chloride channel 3 precursor

-86881166CHIMP_1_224547183.12PREDICTED: Pan troglodytes similar to calcium—activated chloride channel
--HUMAN_1_837766157.82Calcium activated chloride channel 3 precursor
-86881166COW_3_170345139.02Chloride channel, calcium activated, family member 3
-86881166COW_3_170045138.65Epithelial chloride channel protein (Calcium—activated chloride channel)
-86881166DOG_6_162589128.97
-86881166MOUSE_3_2282090123.94Chloride channel calcium activated 4
-86881166RAT_2_220515118.93Calcium—activated chloride channel
-86881166OPOSSUM_2_28758118.77Calcium activated chloride channel 3 precursor
-86881166OPOSSUM_2_28690116.67Calcium activated chloride channel 3 precursor
-86881166RAT_2_220459114.28Chloride channel calcium activated 2
-86881166MOUSE_3_2281377114.18Chloride channel calcium activated 1
-86881166MOUSE_3_2281850110.24Chloride channel calcium activated 2
-86881166COW_3_170620110.22Hypothetical protein (Fragment)
-86881166RAT_2_220748109.88
-86881166MONK_1_36555103.72Calcium activated chloride channel 4
-86881166CHIMP_1_224513103.1Chloride channel, calcium activated, family member 1 precursor
-86881166HUMAN_1_837721103.1Chloride channel, calcium activated, family member 1 precursor
-86881166MOUSE_3_2282601102.32Chloride channel calcium activated 3
-86881166MONK_1_36497102.05Calcium—activated chloride channel family member 1
-86881166COW_3_170508100.32Hypothetical protein LOC507504